The ETE Cookbook¶

This document provides real-case examples, tips and tricks on how to use the ete-tools and the ETE Python API.

This is a work continuously in progress. If you feel like contributing with fixes or new recipes, please get in touch and join us at this cookbook repository.

Tree building (ete-build)¶

• Basic concepts behind ete-build
• Compose custom workflows
• Runninng multiple workflows at once
• Create new workflows and application bindings
• Combining amino-acid and nucleotide sequences

• Using manual alignments

  Species trees:

• Building species trees (Concatenated alignments)

  Available workflows and apps

• List workflows, apps and configurations

  Tips, troubleshooting and debuging:

• Tips and optional arguments
• Details on workflow execution and intermediate data
• Troubleshooting

Testing evolutionary hypothesis (ete-evol)¶

• Testing evolutionary models on branches (Reproducing results from Yang Z (MBE, 1998))
• Testing evolutionary models on sites (Reproducing results from Yang Z (MBE, 2005)
• Testing evolutionary models on sites in a given lineage (Reproducing results from Yang Z (MBE, 2005)
• Running a Codeml from configuration file (running directly PAML examples)